The problem with the rubber liner is that the moisture in the air will wick into the carpet over time and then will condensate out against the liner and keep the carpet just damp enough to allow mold and mildew to thrive. Now that it is there, it will continue to come back everytime there is moisture present. You need to pull all that carpet out the next time you can and spray it with clorox to kill the mold n mildew so it doesn't migrate to the plants or soil.
I keep all my stuff on a raised wood platform(3-6" on small stuff. 8" on my big hydro system, where I have my rez beneath everything) so that air can get beneath it to minimize trapped moisture, and to make it easier to clean up spills.
Let me correct myself by saying take the carpet out and toss it, then spray the floor of the growspace with clorox to kill any spores.